• Most species lineages are young, diverging <10 MYA, during Miocene aridification.

• Further work towards understanding species boundaries in Delma is necessary.

Abstract

Of the more than 1500 species of geckos found across six continents, few remain as unfamiliar as the pygopodids – Family Pygopodidae (Gray, 1845). These gekkotans are limited to Australia (44 species) and New Guinea (2 species), but have diverged extensively into the most ecologically diverse limbless radiation save Serpentes. Current phylogenetic understanding of the family has relied almost exclusively on two works, which have produced and synthesized an immense amount of morphological, geographical, and molecular data. However, current interspecific relationships within the largest genus Delma Gray 1831 are based chiefly upon data from two mitochondrial loci (16s, ND2). Here, we reevaluate the interspecific relationships within the genus Delma using two mitochondrial and four nuclear loci (RAG1, MXRA5, MOS, DYNLL1), and identify points of strong conflict between nuclear and mitochondrial genomic data. We address mito-nuclear discordance, and remedy this conflict by recognizing several points of mitochondrial introgression as the result of ancient hybridization events. Owing to the legacy value and intraspecific informativeness, we suggest the continued use of ND2 as a phylogenetic marker. Results identify strong support for species groups, but relationships among these clades, and the placement of several enigmatic taxa remain uncertain. We suggest a more careful review of Delma australis and the ‘northwest Australia’ clade. Accurately assessing and addressing species richness and relationships within this endemic Australian Gekkotan genus is relevant for understanding patterns of squamate speciation across the region.

Sunday, November 29, 2015

Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1) covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes), and 2) open nests, in which eggs are exposed in the nest and brooded (as in most birds). Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity) of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1) covered nests are likely the primitive condition for dinosaurs (and probably archosaurs), and 2) open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids) were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment. Open nests with fully exposed eggs only became widespread among Euornithes. A potential co-evolution of open nests and brooding behavior among maniraptorans may have freed theropods from the ground-based restrictions inherent to covered nests and allowed the exploitation of alternate nesting locations. These changes in nesting styles and behaviors thus may have played a role in the evolutionary success of maniraptorans (including birds).

The nests of most dinosaurs, including duck-billed hadrosaurs, consisted of eggs covered under mounds of vegetation and dirt. The vegetation mound is not represented in this illustration to display the eggs. (Art by Julius T. Csotonyi.)

A diagram of an archosaur eggshell with high porosity (A) and low porosity (B). Thin slices of the eggs show Caiman latirostris (C), living open nester Pavo cristatus (D), and nonavian dinosaur Troodonformosus (E).

Fig 7. Evolution of nest types among archosaurs.
(A) Phylogeny of archosaurs with inferred nest types based on eggshell porosity and taphonomic evidence. Covered nests are the primitive condition for dinosaurs; open nests and brooding behavior were present among non-avian maniraptoran theropods but may have first appeared earlier. Although the eggs of early open nesters were still partially covered by substrate, open nests with fully exposed eggs likely arose among Euornithes. (B) Phylogeny of Neornithes with inferred nest types based on eggshell porosity (Emeidae) and literature (other birds). Open nests with fully exposed eggs are the primitive condition for modern birds, although secondary reversal to partial egg burial occurred independently in several clades.

The Persian dwarf snake Eirenis (Pseudocyclophis) persicus (Anderson, 1872) has a wide distribution range in south-western Asia. This species group was comprehensively studied here using traditional biometry, geometric morphometrics, ecological niche modelling, and genetics. Our analyses revealed that E. persicus is split into two clades. A western clade, bearing at least two different species: E. persicus, distributed in south-western Iran, and an undescribed species from south-eastern Turkey and western Iran. The eastern clade consists of at least three species: Eirenis nigrofasciatus, distributed across north-eastern Iraq, and western and southern Iran; Eirenis walteri, distributed across eastern Iran, southern Turkmenistan, and western and southern Pakistan, and Eirenis angusticeps, distributed in north-eastern Pakistan. Ecological niche modelling revealed that the distribution of the species in the western clade are mainly affected by winter precipitation, and those in the eastern clade are mainly affected by the minimum temperature of the coldest month. A molecular clock analysis revealed that the divergence and diversification of the E. persicus species group mainly correspond to Eocene to Pliocene orogeny events subsequent to the Arabia–Eurasia collision. This study confirms that specimens with the unique morphology of having 13 dorsal scale rows on the anterior dorsum, occurring in the Suleiman Mountains in central Pakistan, can be referred to Eirenis mcmahoni (Wall, 1911). However, at this moment we have insufficient data to evaluate the taxonomy of this species.

A new lycophyte species, Selaginella chuweimingii, from central Yunnan, China is described and illustrated. Selaginella chuweimingii is similar to S. sinensis in the habit and the morphology of strobili and sporophylls, but the new species can easily be distinguished from the latter by having ovate or oblong-ovate ventral leaves, extremely asymmetrically dorsal leaves, and oblong-ovate to ovate-lanceolate axillary leaves. Also the new species has lamellate ornamentation on megaspore surfaces and less prominent verrucae and ridges on microspore surfaces. The two species are further separated in geographical distribution with the new species occurring in central Yunnan Province while S. sinensis in northern and eastern China.

We describe a new species of Dixonius on the basis of five specimens from Phu Quy Island, Binh Thuan Province, in southern Vietnam. The new species can be distinguished from congeners based on molecular and morphological differences. Diagnostic features are: small size (SVL up to 44 mm); 7 or 8 supralabials; 11 or 12 rows of keeled tubercles on dorsum; 21–23 ventral scale rows; 5 or 6 precloacal pores in males; a canthal stripe running from rostrum through the eye and terminating behind the head; second pair of postmentals about one third to one half size of first pair; ground color of dorsum brown, with one or two rows of light yellow or orange spots in one or two rows along flanks, and irregular bands or a reticulated network of dark marks on dorsum. This is the fifth species of Dixonius known to occur in Vietnam.

Etymology. The new species is named in honor of our colleague and friend Dr. Nguyen Thien Tao from the Vietnam National Museum of Nature in Hanoi, in recognition of his numerous and groundbreaking scientific contributions towards a better understanding of the herpetofauna of Vietnam.

Natural history. The type series were found in secondary forest just above sea level (Fig. 5). The predominant vegetation, which is interspersed with large volcanic stones, consists of small prickly shrubs and species of the families Pandanaceae, Ebenaceae, and Fabaceae. The geckos were collected during a rainy night, when they had left their shelters between stones and shrubs. A few specimens were found in the small shrubs in agricultural lands. Most of the forests in this area have been destroyed, and only a few small patches are left along the coast.

Cycas chenii X. Gong & W. Zhou sp. nov., a new species of Cycas L., is described and illustrated here. The morphological and karyomorphological comparisons are made between C. chenii and the closely related taxa for defining its taxonomical status as a new species. Moreover, the phylogenetic position of C. chenii within 16 Cycas species is determined using DNA sequences of two plastid regions, nuclear ribosomal internal transcribed spacers, and two nuclear regions. Cycas chenii is readily distinguished from the related C. guizhouensis K. M. Lan & R. F. Zou by an acaulescent stem. Phylogenetic evidence indicates that C. chenii is a distinct group related to C. guizhouensis in the Section Stangerioides. The distribution and conservation status of C. chenii are also discussed.

Keywords: China; Cycas chenii; new species; phylogenetic position

Wei Zhou, Meng-Meng Guan and Xun Gong. 2015. Cycas chenii (Cycadaceae), A New Species from China, and its Phylogenetic Position. Journal of Systematics and Evolution. 53(6); 489–498. DOI: 10.1111/jse.12153

Three new species of Annonaceae; Cyathocalyx tsukayae, Mitrephora imbricatarum-apicumand Orophea sagittalis, are described based on materials newly collected from Betung-Kerihun National Park, West Kalimantan, Indonesia.

Brachysaura is a monotypic genus of agamid lizard found in the Indian subcontinent; the identity and systematic position of B. minor has been long debated, and it has at times been subsumed into Agama, Charasia and Laudakia, with some authors suggesting affinities to Calotes. We constructed nuclear and mitochondrial phylogenetic trees including Brachysaura and allied agamid genera to resolve its phylogenetic position. We also compared osteology and external morphology with the genera Agama, Calotes and Laudakia. Hemipenial morphology was compared with Calotes and some other agamids from South Asia. Both nuclear and mitochondrial phylogenies demonstrate that Brachysaura is nested within the widespread South and Southeast Asian genus Calotes, with which it also shares certain external morphological, osteological and hemipenial characters. Adaptations to ground dwelling in Brachysaura minor has resulted in unique modifications to its body plan, which is likely why generic allocation has been long confused. This study also highlights the need for an integrated systematic approach to resolve taxonomic ambiguity in Asian agamids.

Key words: Brachysaura, Calotes, genus, habit, morphology.

Notes on distribution

Brachysaura minor was considered to be one of the widespread species of agamid in the Indian subcontinent. However, most recent and confirmed records on the distribution of B.minor are from western and central India (see Ingle et al. 2012; Khan & Kumar 2010). The record of this species from Angul, Odisha by Chakraborty & Gupta (2009) is that of Psammophilus cf. blanfordianus. The voucher specimen (ZSI 25833) is deposited at the Zoological Survey of India, Calcutta. We identified
this specimen as Psammophilus cf. blanfordianus based
on the small scales on the body and strong fold in the
shoulder region. Additionally, Brachysaura minor have
plate like scales between the eye and above tympanum,
which is missing in this specimen. The only record of B.
minor from eastern part of the subcontinent is the type
locality (Chittagong). Previous authors have raised their
doubts about the occurrence of B. minor in Chittagong
(see Khan & Kumar 2010). We also suspect this record
is erroneous as the habitat at Chittagong is forested with
high rainfall compared to open grassland in semi-arid
and arid regions of western and central India. While rest
of the areas where they occur have mean annual rainfall
between 200–1500 mm, Chittagong has more than
2500 mm mean annual rainfall (Fig. 7). Interestingly, the
closest sister species to Brachysaura minor, Calotes jerdoni
is distributed in North Eastern India, Myanmar and
Bhutan (Smith 1935, Uetz & Hošek 2015).

Fig. 7. Rainfall pattern in the India sub-continent and the distribution of Brachysaura minor.
Red triangle: type locality of B. minor, black triangle: location where Blyth’s specimens were collected; black circles are place where we collected the samples, green circles previous records.

Taxonomic implications

Subsuming Brachysaura into Calotes warrants reassessment of diagnostic characters for the genus Calotes. This is because many of the characters used to differentiate between Pseudocalotes, Calotes and Bronchocela are body ratios (Hallermann & Bӧhme 2000). However B. minor is unique among Calotes in that it has body ratios that are very different from other Calotes spp. This study shows that there are unique hemipenial characters that can be used to diagnose the genus Calotes. Though the osteology of agamids is well documented in Moody (1980), it requires extensive revision in the light of new advances in agamid taxonomy. Further studies are required on both hemipenis and osteology to resolve taxonomic ambiguities and for a better understanding of the evolutionary relationships within Draconinae.

The inclusion of genus Brachysaura to Calotes will not have much taxonomic implications for Brachysaura minor, which becomes Calotes minor(Hardwicke & Gray 1827). Although Gray (1845) listed Agama minor in the synonymy of Calotes minor but the latter is a different agamid, presently considered as Oriocalotes paulus (Günther 1864, Smith 1935, Ananjeva et al. 2011). The specimens of O. paulus referred by Gray (1845) under C. minor were misidentified and they were not types of the new species. The interpretation by Smith (1935) was wrong, which was corrected by Wermuth (1967). Thus the name Calotes minor is not preoccupied and is available for Brachysaura minor.

Conclusions

Convergence in morphological characters driven by its ground dwelling habits probably caused confusion in the genus allocation of Brachysaura minor. This highlights the need to revise diagnostic characters for the genus Calotes. The genus Trapelus and Bufoniceps are the only Agaminae found in Western India. Therefore our finding also limits the distribution of members of Agaminae to the arid regions ( < 500 mm rainfall) of Western India.

The Western Ghats biodiversity hotspot is a recognized center of rhacophorid diversity as demonstrated by several recent studies. The endemic genus Ghatixalus is represented by two species from two separate high-elevation regions within the Ghats. Here, we describe a third species that can be distinguished by morphological and larval characters, as well as by its phylogenetic placement.

Raorchestes flaviventris, a species of rhacophorid bush frog described from the Western Ghats by George Albert Boulenger in 1882, has never been reported from the region since its description. However, we herewith report a record of the species after almost 132 years and redescribe the species and also clarify confusions that prevailed over the taxonomic status of the species and its closely-related congeners, along with shedding light on literature regarding its distribution. Also, the recently described R. emeraldi Vijayakumar et al., 2014, which we suggest to be the same species, becomes a junior subjective synonym of R. flaviventris.

The Urumaco stratigraphic sequence, western Venezuela, preserves a variety of paleoenvironments that include terrestrial, riverine, lacustrine and marine facies. A wide range of fossil vertebrates associated with these facies supports the hypothesis of an estuary in that geographic area connected with a hydrographic system that flowed from western Amazonia up to the Proto-Caribbean Sea during the Miocene. Here the elasmobranch assemblages of the middle Miocene to middle Pliocene section of the Urumaco sequence (Socorro, Urumaco and Codore formations) are described. Based on new findings, we document at least 21 taxa of the Lamniformes, Carcharhiniformes, Myliobatiformes and Rajiformes, and describe a new carcharhiniform species (†Carcharhinus caquetius sp. nov.). Moreover, the Urumaco Formation has a high number of well-preserved fossil Pristis rostra, for which we provide a detailed taxonomic revision, and referral in the context of the global Miocene record of Pristis as well as extant species. Using the habitat preference of the living representatives, we hypothesize that the fossil chondrichthyan assemblages from the Urumaco sequence are evidence for marine shallow waters and estuarine habitats.

Conclusion:

The lithologies of the Urumaco sequence are characterized by substantial variation, indicating the complexity and heterogeneity of these geologic units. Both fossils and the sedimentology document terrestrial and marine facies, including transitional paleoenviroments, and consequently a fauna tolerant to these environments. The elasmobranch fauna from the Urumaco sequence (Socorro-Urumaco-Codore formations), with almost 21 taxa, is associated principally with estuarine coastal lagoon and very shallow marine waters. The presence of elasmobranchs in association with others marine, freshwater and terrestrial vertebrates which provide seemingly contradictory signals for a palaeoenvironmental reconstruction is consistent across the larger stratigraphic sequence. This pattern is not the result of taphonomic processes, but instead proof of mixed coastal marine and fluvial-estuarine hydrographic environments during the Miocene. At the same time, the presence in the Urumaco sequence of abundant aquatic/semiaquatic vertebrates, phylogenetically close to extant groups that occur today in the Orinoco and the Amazon drainage system, support the highly debated hypothesis of a paleo-hydrographic fluvial, lacustrine or wetland complex drainage flowing along the northwestern coast of the Miocene Falcón basin into the proto-Caribbean.

A new species of goby, Lubricogobius nanus, is described from near Alotau, Milne Bay Province, Papua New Guinea on the basis of four adult specimens, 9.5–10.9 mm SL. Diagnostic features include 10–11 segmented dorsal-fin rays, 8–9 segmented anal-fin rays, the presence of both anterior and posterior nostrils, a low fleshy keel mid-dorsally and mid-ventrally on the caudal peduncle, a mid-lateral row of widely-spaced sensory papillae on the side of the body, approximately 15 scattered sensory papillae on the middle portion of the caudal fin, body depth 3.2–3.4 in SL, mainly brown coloration with yellow fins, and an exceptionally small size (<11 mm SL). Photographs and comparative morphological data are presented for the other four members of the genus, including L.dinah, L. exiguus, L. ornatus, and L. tre.

We describe a new species from the family Salamandridae from northeastern Hunan Province of China based on morphological and molecular genetic evidences. The new species, Tylototriton liuyangensis,is a member of the T. asperrimus group,and shares a number of similarities with T. wenxianensis and T. broadoridgus.The dorsal surface of the new Tylototriton species is completely black,with nodule-like warts distributed evenly along the lateral margin of dorsal body,and there is no transverse striae between the warts.There are several diagnostic characters of the new species that differ from those of T. wenxianensis and T. broadoridgus as follows: (1) the interorbital space (IOS) is comparatively wide; (2) there is a bony ridge present on the dorsal head surface,running along the upper eyelids; (3) the space between axilla and groin (AGS) is comparatively large,with the mean male AGS approximately equal to 50%of the snout-vent length (SVL) and the mean female AGS being 53%of SVL; and (4) there is a small genital armature on the anterior angle of labial folds present inside the anal fissure of adult males during the breeding season.The result from the molecular phylogenetic analysis of the genus Tylototriton (including the type specimen of the new species)based on the complete DNA sequence of the mitochondrial ND2 gene(1035 bp)indicated that the new species was similar to T. wenxianensis, T. dabienicus, and T. broadoridgus, but formed an independent clade.This result was consistent with the morphological analysis above, supporting that the Liuyang Population represented a distinct species.

A new species of troglobitic harvestman,Iandumoema smeagol sp. n., is described from Toca do Geraldo, Monjolos municipality, Minas Gerais state, Brazil. Iandumoema smeagol sp. n. is distinguished from the other two species of the genus by four exclusive characteristics – dorsal scutum areas with conspicuous tubercles, enlarged retrolateral spiniform tubercle on the distal third of femur IV, eyes absent and the penial ventral process slender and of approximately the same length of the stylus. The species is the most highly modified in the genus and its distribution is restricted only to caves in that particular area of Minas Gerais state. The type locality is not inside a legally protected area, and there are anthropogenic impacts in its surroundings. Therefore, Iandumoema smeagol sp. n. is vulnerable and it must be considered in future conservation projects.

Etymology: The specific epithet refers to the hobbit named Smeagol, created by J.R.R. Tolkien, being the original name of Gollum – the dweller of the caves located below the Misty Mountains of Middle-earth of the Lord of the Rings book.

Distribution and natural history

The occurrence of Iandumoema smeagol sp. n. in the limestone caves of Bambuí Group, more specifically in the boundaries of Serra do Espinhaço Plateau (Figure 1) shows that this region must be the eastern boundary distribution of the genus, the quartzite and the high altitudes of Serra do Espinhaço being the possible barriers. The results show that the genus Iandumoema only occurs in the northern Minas Gerais state, occupying an area of ca. 8,000 km2, and is restricted to hypogean environments, being exclusive to caves. This distribution range corroborates those presented by Hara and Pinto-da-Rocha (2008). Most specimens were collected in the aphotic zone of Toca do Geraldo cave; and only one individual was recorded in the Lapa do Santo Antônio cave. The minimum distribution range for Iandumoema smeagol sp. n. (or occurrence area) is of 4.6 km2. The specimen collected in the Lapa do Santo Antônio cave was on the rocky substrate, at the twilight zone and close to the entrance (less than 50 m away). In four visits at Toca do Geraldo, the opilionids were observed on the walls (rocky substrate) and few on the silt substrate, always close to water bodies (drainage or pools). Despite the observed guano piles (of hematophagous bats), not one individual was observed close to them. The adults show solitary habits; on one occasion, one individual was feeding in litter, apparently scavenging carcasses of invertebrates (Figure 12). In two occasions, active juveniles were observed on the walls while the adults showed a behavior comparatively more sedentary. In the four occasions, a total of 14 individuals were observed including adults and juveniles, always close to the cave stream, showing a low abundance. Apparently, the cave does not have dry galleries and/or conduits, showing high relative humidity of the air (ca. 80%) and temperature amplitude between 22 and 24 °C.

As a result of their faunistic singularities and high endemism, hypogean environments are considered fragile. Besides their unique faunistic composition, the singularity of cave habitats is related to the presence of relicts, many times represented by troglobitic species. Gallão and Bichuette (2015) observed this tendency in a small area (24 km2) located at Chapada Diamantina, northeastern Brazil (at least 23 troglobitic species, most of them relict ones). Troglobitic species have unique sets of autapomorphies, such as eyes and melanistic pigmentation reductions allied to other troglomorphisms, such as pedipalps elongation in opilionids and other arachnids. A possible endemism in a karst area, which is threatened, was observed for Iandumoema smeagol sp. n. in addition to the accentuated autapomorphies. Projects for the installation of small hydroelectric dams and limestone extraction for cement production represent potential impacts on the immediate environment (M. E. Bichuette and R. Fonseca-Ferreira, pers. obs.). Moreover, the extent of occurrence area of the species (4.6 sq.km.) allied to the deforestation in the cave surroundings must place this species in a threatened category considering the IUCN criteria (Vulnerable, VU or Endangered, EN). Long-term studies focusing population biology and distribution of I. smeagol sp. n. are urgent and fundamental to establish an effective conservation policy, including the creation of protected area(s).

Wednesday, November 18, 2015

Fig. 2. Lesser Moorhen Paragallinula angulata Sundevall, 1850, Kgomo Kgomo, South Africa, Feb. 2011 (photo by Mark Tittley).
This photograph illustrates two diagnostic character states differentiating Paragallinula from the genus Gallinula: the orange colouration on the frontal shield does not cover the entire shield, and the lack of a contrasting reddish band on the legs proximal to the ankle joint.

Molecular phylogenetic analysis has demonstrated that the genus Gallinula is not monophyletic and comprises four major lineages. A review of the nomenclature of Gallinula shows that generic names are available for three lineages but that a fourth is as yet unnamed. A new monotypic genus, Paragallinula gen. nov., is described for Lesser Moorhen (Gallinula angulata Sundevall, 1850).

Etymology: The generic name is derived from the Greek para (beside) and the Latin gallinula (a little hen or chicken). It denotes the resemblance of P. angulata to species of Gallinula but highlights that they are independent evolutionary lineages. The gender of the name is feminine.

Distribution: Paragallinula angulata is found in most of the African continent from Senegal and Gambia to Ethiopia, Namibia, Botswana and South Africa.